RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10055
(124 letters)
>gnl|CDD|236448 PRK09281, PRK09281, F0F1 ATP synthase subunit alpha; Validated.
Length = 502
Score = 72.8 bits (180), Expect = 3e-16
Identities = 23/24 (95%), Positives = 24/24 (100%)
Query: 100 RELIIGDRQTGKTALAIDTIINQK 123
RELIIGDRQTGKTA+AIDTIINQK
Sbjct: 164 RELIIGDRQTGKTAIAIDTIINQK 187
>gnl|CDD|223134 COG0056, AtpA, F0F1-type ATP synthase, alpha subunit [Energy
production and conversion].
Length = 504
Score = 67.6 bits (166), Expect = 2e-14
Identities = 23/25 (92%), Positives = 24/25 (96%)
Query: 100 RELIIGDRQTGKTALAIDTIINQKR 124
RELIIGDRQTGKTA+AIDTIINQK
Sbjct: 164 RELIIGDRQTGKTAIAIDTIINQKG 188
>gnl|CDD|238552 cd01132, F1_ATPase_alpha, F1 ATP synthase alpha, central domain.
The F-ATPase is found in bacterial plasma membranes,
mitochondrial inner membranes and in chloroplast
thylakoid membranes. It has also been found in the
archaea Methanosarcina barkeri. It uses a proton
gradient to drive ATP synthesis and hydrolyzes ATP to
build the proton gradient. The extrinisic membrane
domain, F1, is composed of alpha, beta, gamma, delta and
epsilon subunits with a stoichiometry of 3:3:1:1:1. The
alpha subunit of the F1 ATP synthase can bind
nucleotides, but is non-catalytic.
Length = 274
Score = 65.4 bits (160), Expect = 7e-14
Identities = 23/25 (92%), Positives = 24/25 (96%)
Query: 100 RELIIGDRQTGKTALAIDTIINQKR 124
RELIIGDRQTGKTA+AIDTIINQK
Sbjct: 71 RELIIGDRQTGKTAIAIDTIINQKG 95
>gnl|CDD|176999 CHL00059, atpA, ATP synthase CF1 alpha subunit.
Length = 485
Score = 65.4 bits (160), Expect = 1e-13
Identities = 21/24 (87%), Positives = 23/24 (95%)
Query: 100 RELIIGDRQTGKTALAIDTIINQK 123
RELIIGDRQTGKTA+A DTI+NQK
Sbjct: 143 RELIIGDRQTGKTAVATDTILNQK 166
>gnl|CDD|183987 PRK13343, PRK13343, F0F1 ATP synthase subunit alpha; Provisional.
Length = 502
Score = 64.6 bits (158), Expect = 2e-13
Identities = 22/24 (91%), Positives = 23/24 (95%)
Query: 100 RELIIGDRQTGKTALAIDTIINQK 123
RELIIGDRQTGKTA+AID IINQK
Sbjct: 164 RELIIGDRQTGKTAIAIDAIINQK 187
>gnl|CDD|233211 TIGR00962, atpA, proton translocating ATP synthase, F1 alpha
subunit. The sequences of ATP synthase F1 alpha and
beta subunits are related and both contain a
nucleotide-binding site for ATP and ADP. They have a
common amino terminal domain but vary at the C-terminus.
The beta chain has catalytic activity, while the alpha
chain is a regulatory subunit. The alpha-subunit
contains a highly conserved adenine-specific
noncatalytic nucleotide-binding domain. The conserved
amino acid sequence is Gly-X-X-X-X-Gly-Lys. Proton
translocating ATP synthase F1, alpha subunit is
homologous to proton translocating ATP synthase
archaeal/vacuolar(V1), B subunit [Energy metabolism,
ATP-proton motive force interconversion].
Length = 501
Score = 62.0 bits (151), Expect = 2e-12
Identities = 23/24 (95%), Positives = 24/24 (100%)
Query: 100 RELIIGDRQTGKTALAIDTIINQK 123
RELIIGDRQTGKTA+AIDTIINQK
Sbjct: 163 RELIIGDRQTGKTAVAIDTIINQK 186
>gnl|CDD|235951 PRK07165, PRK07165, F0F1 ATP synthase subunit alpha; Validated.
Length = 507
Score = 58.8 bits (143), Expect = 2e-11
Identities = 20/25 (80%), Positives = 23/25 (92%)
Query: 100 RELIIGDRQTGKTALAIDTIINQKR 124
RELIIGDRQTGKT +A++TIINQK
Sbjct: 145 RELIIGDRQTGKTHIALNTIINQKN 169
>gnl|CDD|132367 TIGR03324, alt_F1F0_F1_al, alternate F1F0 ATPase, F1 subunit alpha.
A small number of taxonomically diverse prokaryotic
species, including Methanosarcina barkeri, have what
appears to be a second ATP synthase, in addition to the
normal F1F0 ATPase in bacteria and A1A0 ATPase in
archaea. These enzymes use ion gradients to synthesize
ATP, and in principle may run in either direction. This
model represents the F1 alpha subunit of this apparent
second ATP synthase.
Length = 497
Score = 56.3 bits (136), Expect = 2e-10
Identities = 21/24 (87%), Positives = 24/24 (100%)
Query: 100 RELIIGDRQTGKTALAIDTIINQK 123
RELI+GDRQTGKTA+AIDTI+NQK
Sbjct: 164 RELILGDRQTGKTAIAIDTILNQK 187
>gnl|CDD|140212 PTZ00185, PTZ00185, ATPase alpha subunit; Provisional.
Length = 574
Score = 47.7 bits (113), Expect = 2e-07
Identities = 19/25 (76%), Positives = 23/25 (92%)
Query: 100 RELIIGDRQTGKTALAIDTIINQKR 124
RELI+GDRQTGKT++A+ TIINQ R
Sbjct: 191 RELIVGDRQTGKTSIAVSTIINQVR 215
>gnl|CDD|215651 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
nucleotide-binding domain. This family includes the ATP
synthase alpha and beta subunits, the ATP synthase
associated with flagella and the termination factor Rho.
Length = 213
Score = 42.1 bits (100), Expect = 1e-05
Identities = 10/24 (41%), Positives = 10/24 (41%)
Query: 100 RELIIGDRQTGKTALAIDTIINQK 123
R I G TGKT L N K
Sbjct: 17 RIGIFGGSGTGKTVLLGMIARNAK 40
>gnl|CDD|238011 cd00054, EGF_CA, Calcium-binding EGF-like domain, present in a
large number of membrane-bound and extracellular
(mostly animal) proteins. Many of these proteins
require calcium for their biological function and
calcium-binding sites have been found to be located at
the N-terminus of particular EGF-like domains;
calcium-binding may be crucial for numerous
protein-protein interactions. Six conserved core
cysteines form three disulfide bridges as in non
calcium-binding EGF domains, whose structures are very
similar. EGF_CA can be found in tandem repeat
arrangements.
Length = 38
Score = 36.5 bits (85), Expect = 1e-04
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 27 DPCEEHDPCKHGGICISTDSGPICECRNLDFEGIYCE 63
D C +PC++GG C++T C C + G CE
Sbjct: 3 DECASGNPCQNGGTCVNTVGSYRCSCPP-GYTGRNCE 38
>gnl|CDD|215652 pfam00008, EGF, EGF-like domain. There is no clear separation
between noise and signal. pfam00053 is very similar,
but has 8 instead of 6 conserved cysteines. Includes
some cytokine receptors. The EGF domain misses the
N-terminus regions of the Ca2+ binding EGF domains
(this is the main reason of discrepancy between
swiss-prot domain start/end and Pfam). The family is
hard to model due to many similar but different
sub-types of EGF domains. Pfam certainly misses a
number of EGF domains.
Length = 32
Score = 32.8 bits (75), Expect = 0.003
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 29 CEEHDPCKHGGICISTDSGPICEC 52
C ++PC +GG C+ T G CEC
Sbjct: 1 CSPNNPCSNGGTCVDTPGGYTCEC 24
>gnl|CDD|214542 smart00179, EGF_CA, Calcium-binding EGF-like domain.
Length = 39
Score = 33.0 bits (76), Expect = 0.003
Identities = 14/37 (37%), Positives = 20/37 (54%)
Query: 27 DPCEEHDPCKHGGICISTDSGPICECRNLDFEGIYCE 63
D C +PC++GG C++T CEC +G CE
Sbjct: 3 DECASGNPCQNGGTCVNTVGSYRCECPPGYTDGRNCE 39
>gnl|CDD|238010 cd00053, EGF, Epidermal growth factor domain, found in epidermal
growth factor (EGF) presents in a large number of
proteins, mostly animal; the list of proteins currently
known to contain one or more copies of an EGF-like
pattern is large and varied; the functional
significance of EGF-like domains in what appear to be
unrelated proteins is not yet clear; a common feature
is that these repeats are found in the extracellular
domain of membrane-bound proteins or in proteins known
to be secreted (exception: prostaglandin G/H synthase);
the domain includes six cysteine residues which have
been shown to be involved in disulfide bonds; the main
structure is a two-stranded beta-sheet followed by a
loop to a C-terminal short two-stranded sheet;
Subdomains between the conserved cysteines vary in
length; the region between the 5th and 6th cysteine
contains two conserved glycines of which at least one
is present in most EGF-like domains; a subset of
these bind calcium.
Length = 36
Score = 32.1 bits (73), Expect = 0.006
Identities = 9/27 (33%), Positives = 13/27 (48%)
Query: 28 PCEEHDPCKHGGICISTDSGPICECRN 54
C +PC +GG C++T C C
Sbjct: 1 ECAASNPCSNGGTCVNTPGSYRCVCPP 27
>gnl|CDD|232841 TIGR00131, gal_kin, galactokinase. Galactokinase is a member of
the GHMP kinases (Galactokinase, Homoserine kinase,
Mevalonate kinase, Phosphomevalonate kinase) and shares
with them an amino-terminal domain probably related to
ATP binding.The galactokinases found by This model are
divided into two sets. Prokaryotic forms are generally
shorter. The eukaryotic forms are longer because of
additional central regions and in some cases are known
to be bifunctional, with regulatory activities that are
independent of galactokinase activity [Energy
metabolism, Sugars].
Length = 386
Score = 30.2 bits (68), Expect = 0.25
Identities = 13/46 (28%), Positives = 18/46 (39%), Gaps = 3/46 (6%)
Query: 51 ECRNLDFEGIYCEKVEISVVRAISMRVR---GSRKKLRLIECEDGA 93
ECR+L ++ I+ V A + R S R EC A
Sbjct: 188 ECRSLKATPFKFPQLGIAFVIANTNVKRTLAPSNYNTRRQECTTAA 233
>gnl|CDD|214544 smart00181, EGF, Epidermal growth factor-like domain.
Length = 35
Score = 27.1 bits (60), Expect = 0.44
Identities = 9/27 (33%), Positives = 11/27 (40%), Gaps = 1/27 (3%)
Query: 28 PCEEHDPCKHGGICISTDSGPICECRN 54
C PC +G CI+T C C
Sbjct: 1 ECASGGPCSNG-TCINTPGSYTCSCPP 26
>gnl|CDD|182754 PRK10815, PRK10815, sensor protein PhoQ; Provisional.
Length = 485
Score = 29.2 bits (66), Expect = 0.52
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 9/44 (20%)
Query: 61 YC-EKVEISVVRAISMRVRGSRKKLRLIECEDGAGMDPPSRELI 103
YC E VEIS R + + L ++ +DG G+ RELI
Sbjct: 393 YCLEFVEISA--------RQTDEHLHIVVEDDGPGIPESKRELI 428
>gnl|CDD|238540 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
the NTP binding domain of F1 and V1 H+ATPases, DnaB and
related helicases as well as bacterial RecA and related
eukaryotic and archaeal recombinases. This group also
includes bacterial conjugation proteins and related DNA
transfer proteins involved in type II and type IV
secretion.
Length = 165
Score = 28.2 bits (63), Expect = 0.77
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 100 RELIIGDRQTGKTALAIDTIINQKR 124
L+ G +GKT LA+ +N
Sbjct: 1 LILVFGPTGSGKTTLALQLALNIAT 25
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 28.1 bits (63), Expect = 1.4
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 102 LIIGDRQTGKTALAI 116
LI+G TGKTALA+
Sbjct: 69 LIVGPPGTGKTALAM 83
>gnl|CDD|233208 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family protein.
[Transport and binding proteins, Other].
Length = 1394
Score = 27.8 bits (62), Expect = 1.8
Identities = 10/26 (38%), Positives = 12/26 (46%), Gaps = 3/26 (11%)
Query: 3 ENRNCTALCSDCQYCHYSVENSVLDP 28
N N T C +C YS N L+P
Sbjct: 1335 LNPNAT---DSCSFCQYSYTNDFLEP 1357
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 27.0 bits (60), Expect = 2.6
Identities = 12/22 (54%), Positives = 14/22 (63%)
Query: 94 GMDPPSRELIIGDRQTGKTALA 115
G+DPP L+ G TGKT LA
Sbjct: 175 GIDPPRGVLLYGPPGTGKTMLA 196
>gnl|CDD|238649 cd01328, FSL_SPARC, Follistatin-like SPARC (secreted protein,
acidic, and rich in cysteines) domain;
SPARC/BM-40/osteonectin is a multifunctional
glycoprotein which modulates cellular interaction with
the extracellular matrix by its binding to structural
matrix proteins such as collagen and vitronectin. The
protein it composed of an N-terminal acidic region, a
follistatin (FS) domain and an EF-hand calcium binding
domain. The FS domain consists of an N-terminal beta
hairpin (FOLN/EGF-like domain) and a small hydrophobic
core of alpha/beta structure (Kazal domain) and has
five disulfide bonds and a conserved N-glycosylation
site. The FSL_SPARC domain is a member of the
superfamily of kazal-like proteinase inhibitors and
follistatin-like proteins.
Length = 86
Score = 25.9 bits (57), Expect = 2.8
Identities = 11/26 (42%), Positives = 12/26 (46%), Gaps = 2/26 (7%)
Query: 28 PCEEHDPCKHGGICISTDSG-PICEC 52
PCE H C G +C D P C C
Sbjct: 1 PCENH-HCGAGKVCEVDDENTPKCVC 25
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 154
Score = 26.8 bits (59), Expect = 2.8
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 102 LIIGDRQTGKTALA 115
L+ G TGKT+L
Sbjct: 28 LLTGPSGTGKTSLL 41
>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the
C-terminal region of several eukaryotic and archaeal
RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
or TIP49b) proteins. The N-terminal domain contains the
pfam00004 domain. In zebrafish, the liebeskummer (lik)
mutation, causes development of hyperplastic embryonic
hearts. lik encodes Reptin, a component of a
DNA-stimulated ATPase complex. Beta-catenin and Pontin,
a DNA-stimulated ATPase that is often part of complexes
with Reptin, are in the same genetic pathways. The
Reptin/Pontin ratio serves to regulate heart growth
during development, at least in part via the
beta-catenin pathway. TBP-interacting protein 49 (TIP49)
was originally identified as a TBP-binding protein, and
two related proteins are encoded by individual genes,
tip49a and b. Although the function of this gene family
has not been elucidated, they are supposed to play a
critical role in nuclear events because they interact
with various kinds of nuclear factors and have DNA
helicase activities.TIP49a has been suggested to act as
an autoantigen in some patients with autoimmune
diseases.
Length = 395
Score = 26.9 bits (60), Expect = 3.0
Identities = 11/15 (73%), Positives = 11/15 (73%)
Query: 102 LIIGDRQTGKTALAI 116
LI G TGKTALAI
Sbjct: 54 LIAGPPGTGKTALAI 68
>gnl|CDD|172310 PRK13772, PRK13772, formimidoylglutamase; Provisional.
Length = 314
Score = 26.6 bits (59), Expect = 3.5
Identities = 10/22 (45%), Positives = 13/22 (59%), Gaps = 1/22 (4%)
Query: 65 VEISVVRAISMRVRGSRKKLRL 86
V + VV I + VR S KLR+
Sbjct: 266 VPLPVVEEIVLHVRAS-GKLRV 286
>gnl|CDD|222680 pfam14323, GxGYxYP, GxGYxY sequence motif in domain of unknown
function. This family carries a characteristic sequence
motif, GxGYxYP, but is of unknown function. Associated
families are sugar-processing domains.
Length = 463
Score = 26.1 bits (58), Expect = 5.3
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 38 GGICISTDSGPICECRNLDFEGIYCE 63
G I +S P+ CR L + G+ E
Sbjct: 373 GRITWYRNSKPVISCRYLLWGGLEDE 398
>gnl|CDD|215497 PLN02919, PLN02919, haloacid dehalogenase-like hydrolase family
protein.
Length = 1057
Score = 26.4 bits (58), Expect = 5.5
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 56 DFEGIYCEKVEISVVRAISMRVRGSR 81
D + +Y E S +RA+ ++ GSR
Sbjct: 750 DLKELYIADSESSSIRALDLKTGGSR 775
>gnl|CDD|221017 pfam11185, DUF2971, Protein of unknown function (DUF2971). This
bacterial family of proteins has no known function.
Length = 82
Score = 25.2 bits (55), Expect = 5.7
Identities = 8/30 (26%), Positives = 11/30 (36%), Gaps = 1/30 (3%)
Query: 37 HGGICISTDSGPICECRNLDFEGIYCEKVE 66
H G+ I D + + N IY V
Sbjct: 9 HKGVAIEFDKEELLKLEN-SDSEIYLGPVI 37
>gnl|CDD|224260 COG1341, COG1341, Predicted GTPase or GTP-binding protein [General
function prediction only].
Length = 398
Score = 26.2 bits (58), Expect = 5.8
Identities = 4/34 (11%), Positives = 11/34 (32%)
Query: 83 KLRLIECEDGAGMDPPSRELIIGDRQTGKTALAI 116
++ +++G +GK+ L
Sbjct: 58 EIADTWESKSESAGKVGVVMVVGPVDSGKSTLTT 91
>gnl|CDD|237793 PRK14703, PRK14703, glutaminyl-tRNA synthetase/YqeY domain fusion
protein; Provisional.
Length = 771
Score = 26.2 bits (58), Expect = 6.0
Identities = 17/52 (32%), Positives = 22/52 (42%)
Query: 71 RAISMRVRGSRKKLRLIECEDGAGMDPPSRELIIGDRQTGKTALAIDTIINQ 122
A+ V RK L+E +G D P I G R+ G T AI +Q
Sbjct: 267 LALGYTVMSKRKLRELVEEGYVSGWDDPRMPTIAGQRRRGVTPEAIRDFADQ 318
>gnl|CDD|213190 cd03223, ABCD_peroxisomal_ALDP, ATP-binding cassette domain of
peroxisomal transporter, subfamily D. Peroxisomal
ATP-binding cassette transporter (Pat) is involved in
the import of very long-chain fatty acids (VLCFA) into
the peroxisome. The peroxisomal membrane forms a
permeability barrier for a wide variety of metabolites
required for and formed during fatty acid
beta-oxidation. To communicate with the cytoplasm and
mitochondria, peroxisomes need dedicated proteins to
transport such hydrophilic molecules across their
membranes. X-linked adrenoleukodystrophy (X-ALD) is
caused by mutations in the ALD gene, which encodes ALDP
(adrenoleukodystrophy protein ), a peroxisomal integral
membrane protein that is a member of the ATP-binding
cassette (ABC) transporter protein family. The disease
is characterized by a striking and unpredictable
variation in phenotypic expression. Phenotypes include
the rapidly progressive childhood cerebral form (CCALD),
the milder adult form, adrenomyeloneuropathy (AMN), and
variants without neurologic involvement (i.e.
asymptomatic).
Length = 166
Score = 25.6 bits (57), Expect = 6.1
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 95 MDPPSRELIIGDRQTGKTAL 114
+ P R LI G TGK++L
Sbjct: 24 IKPGDRLLITGPSGTGKSSL 43
>gnl|CDD|234401 TIGR03925, T7SS_EccC_b, type VII secretion protein EccCb. This
model represents the C-terminal domain or EccCb subunit
of the type VII secretion protein EccC as found in the
Actinobacteria. Type VII secretion is defined more
broadly as including secretion systems for ESAT-6-like
proteins in the Firmicutes as well as in the
Actinobacteria, but this family does not show close
homologs in the Firmicutes [Protein fate, Protein and
peptide secretion and trafficking].
Length = 566
Score = 25.7 bits (57), Expect = 7.2
Identities = 7/13 (53%), Positives = 10/13 (76%)
Query: 102 LIIGDRQTGKTAL 114
L+ GD ++GKT L
Sbjct: 367 LVFGDSESGKTTL 379
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 25.2 bits (56), Expect = 7.4
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 102 LIIGDRQTGKTALAIDTI 119
+I G RQ GKT L + +
Sbjct: 6 VITGPRQVGKTTLLLQFL 23
>gnl|CDD|213237 cd03270, ABC_UvrA_I, ATP-binding cassette domain I of the excision
repair protein UvrA. Nucleotide excision repair in
eubacteria is a process that repairs DNA damage by the
removal of a 12-13-mer oligonucleotide containing the
lesion. Recognition and cleavage of the damaged DNA is a
multistep ATP-dependent reaction that requires the UvrA,
UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases,
with UvrA having two ATP binding sites, which have the
characteristic signature of the family of ABC proteins,
and UvrB having one ATP binding site that is
structurally related to that of helicases.
Length = 226
Score = 25.3 bits (56), Expect = 9.6
Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 9/47 (19%)
Query: 76 RVRGSR-KKLRLIECEDGAGMDPPSRELII--GDRQTGKTALAIDTI 119
VRG+R L+ ++ +D P +L++ G +GK++LA DTI
Sbjct: 2 IVRGAREHNLKNVD------VDIPRNKLVVITGVSGSGKSSLAFDTI 42
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.137 0.432
Gapped
Lambda K H
0.267 0.0632 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,887,732
Number of extensions: 494223
Number of successful extensions: 493
Number of sequences better than 10.0: 1
Number of HSP's gapped: 491
Number of HSP's successfully gapped: 48
Length of query: 124
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 39
Effective length of database: 7,167,512
Effective search space: 279532968
Effective search space used: 279532968
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.4 bits)